Ok, I've done some troubleshooting on this already, but in short after upgrading to 6.9 all drives attached to my sata card disappear.  Reverting (and fixing the cache config) restores functionality.

 

At this point I've tried playing with the IOMMU setting in syslinux.cfg, which was set to PT originally, but have found only that setting it to ON breaks the card on 6.8.  This setting has no effect on the behavior on 6.9.

 

IOMMU groups are:

-its the Marvell controller giving issues, but bear in mind that it's not reporting as bound to VFIO, disappearing in its own right or causing errors in the log under 6.9

 

IOMMU group 0:  [8086:0100] 00:00.0 Host bridge: Intel Corporation 2nd Generation Core Processor Family DRAM Controller (rev 09)
IOMMU group 1:  [8086:0101] 00:01.0 PCI bridge: Intel Corporation Xeon E3-1200/2nd Generation Core Processor Family PCI Express Root Port (rev 09) 
                [1b4b:9230] 01:00.0 SATA controller: Marvell Technology Group Ltd. 88SE9230 PCIe SATA 6Gb/s Controller (rev 11)
IOMMU group 2:  [8086:0102] 00:02.0 VGA compatible controller: Intel Corporation 2nd Generation Core Processor Family Integrated Graphics Controller (rev 09)
IOMMU group 3:  [8086:1e31] 00:14.0 USB controller: Intel Corporation 7 Series/C210 Series Chipset Family USB xHCI Host Controller (rev 04)
IOMMU group 4:  [8086:1e3a] 00:16.0 Communication controller: Intel Corporation 7 Series/C216 Chipset Family MEI Controller #1 (rev 04)
IOMMU group 5:  [8086:1e2d] 00:1a.0 USB controller: Intel Corporation 7 Series/C216 Chipset Family USB Enhanced Host Controller #2 (rev 04)
IOMMU group 6:  [8086:1e20] 00:1b.0 Audio device: Intel Corporation 7 Series/C216 Chipset Family High Definition Audio Controller (rev 04)
IOMMU group 7:  [8086:1e10] 00:1c.0 PCI bridge: Intel Corporation 7 Series/C216 Chipset Family PCI Express Root Port 1 (rev c4)
IOMMU group 8:  [8086:1e18] 00:1c.4 PCI bridge: Intel Corporation 7 Series/C210 Series Chipset Family PCI Express Root Port 5 (rev c4)
IOMMU group 9:  [8086:1e26] 00:1d.0 USB controller: Intel Corporation 7 Series/C216 Chipset Family USB Enhanced Host Controller #1 (rev 04)
IOMMU group 10: [8086:244e] 00:1e.0 PCI bridge: Intel Corporation 82801 PCI Bridge (rev a4)
IOMMU group 11: [8086:1e49] 00:1f.0 ISA bridge: Intel Corporation B75 Express Chipset LPC Controller (rev 04)
                [8086:1e00] 00:1f.2 IDE interface: Intel Corporation 7 Series/C210 Series Chipset Family 4-port SATA Controller [IDE mode] (rev 04)
                [8086:1e22] 00:1f.3 SMBus: Intel Corporation 7 Series/C216 Chipset Family SMBus Controller (rev 04)
                [8086:1e08] 00:1f.5 IDE interface: Intel Corporation 7 Series/C210 Series Chipset Family 2-port SATA Controller [IDE mode] (rev 04)
IOMMU group 12: [10ec:8168] 03:00.0 Ethernet controller: Realtek Semiconductor Co., Ltd. RTL8111/8168/8411 PCI Express Gigabit Ethernet Controller (rev 06)

 

My working syslinux.cfg is:

 

default menu.c32
menu title Lime Technology, Inc.
prompt 0
timeout 50
label unRAID OS
  menu default
  kernel /bzimage
  append initrd=/bzroot iommu=pt kvm-amd.npt=0 kvm.ignore_msrs=1
label unRAID OS GUI Mode
  kernel /bzimage
  append initrd=/bzroot,/bzroot-gui
label unRAID OS Safe Mode (no plugins, no GUI)
  kernel /bzimage
  append initrd=/bzroot unraidsafemode
label unRAID OS GUI Safe Mode (no plugins)
  kernel /bzimage
  append initrd=/bzroot,/bzroot-gui unraidsafemode
label Memtest86+
  kernel /memtest

 

Probably not what you want to hear bu IMHO best bet would be to replace that Marvell controller with one of the recommended models.